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Genome Biology DOI:

A strategy for oligonucleotide microarray probe reduction

Publication TypeJournal Article
Year of Publication2002
AuthorsAntipova, AA, Tamayo, P, Golub, TR
JournalGenome Biology
Date Published2002///
ISBN Number1465-6914
KeywordsAcute Disease, B-Cell, Cancer, Cerebellar Neoplasms, Diffuse, DNA, Expressed Sequence Tags, Genes, Humans, Large B-Cell, Leukemia, Lymphoma, Medulloblastoma, Myeloid, Neoplasm, Nucleic Acid Probes, Oligonucleotide Array Sequence Analysis, Prec

BACKGROUND: One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number of probes required for each gene, a systematic approach to choosing the most representative probes is needed. A method is presented for reducing the number of probes per gene while maximizing the fidelity to the original array design. RESULTS: The methodology has been tested on a dataset comprising 317 Affymetrix HuGeneFL GeneChips. The performance of the original and reduced probe sets was compared in four cancer-classification problems. The results of these comparisons show that reduction of the probe set by 95% does not dramatically affect performance, and thus illustrate the feasibility of substantially reducing probe numbers without significantly compromising sensitivity and specificity of detection. CONCLUSIONS: The strategy described here is potentially useful for designing small, limited-probe genome-wide arrays for screening applications.